[gmx-users] Expanded Ensemble and Gromacs 4.6
mrshirts at gmail.com
Tue Feb 5 16:06:21 CET 2013
Expanded ensemble is still a bit experimental. I don't immediately
see any problem that jump right out, but if you go to
http://redmine.gromacs.org/ and file a bug report, including giving
example files that cause the problem, I can take a look at it.
On Tue, Feb 5, 2013 at 6:00 AM, Joakim Jämbeck <jambeck at me.com> wrote:
> I am trying to use the Expanded Ensemble (EE) method to compute the free energy of solvation of a small organic molecule.
> Basically I am playing around but I cannot get the simulations to run.
> Here are my EE and free energy settings:
> free-energy = expanded ; Expanded ensemble
> couple-moltype = C1X ; Molecule to introduce
> couple-lambda0 = none ; Go from no interactions with solvent...
> couple-lambda1 = vdw-q ; ...to full interactions
> couple-intramol = no ; Do not decouple internal interactions
> init_lambda_state = 0 ; Start from the first column of the lambda vectors
> delta-lambda = 0 ; No increments in lambda
> nstdhdl = 100 ; Frequency for writing dH/dlambda
> coul-lambdas = 0.0 0.25 0.5 0.75 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
> vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.2 0.4 0.6 0.7 0.8 0.9 1.0
> dhdl-print-energy = yes ; Include total energy in the dhdl file
> sc-alpha = 0.5 ; Soft core alpha parameter
> sc-power = 1 ; Power of lambda in soft core function
> sc-r-power = 6 ; Power of radial term in the soft core function
> sc-sigma = 0.3 ; Soft core sigma
> sc-coul = no ; No soft core for Coulomb
> separate-dhdl-file = yes ; Seperate dhdl files
> dhdl-derivatives = yes ; Print derivatives of the Hamiltonian
> ; expanded ensemble variables
> nstexpanded = 100 ; Number of steps between attempts to change the Hamiltonian
> lmc-stats = wang-landau ; WL algorithm to explore state space
> lmc-move = gibbs ; Decides which state to move to
> lmc-weights-equil = number-steps ; EE weight updating stops after...
> weight-equil-number-steps = 5000000 ; ...10ns of simulation
> ; Seed for Monte Carlo in lambda space
> lmc-seed = 1993
> lmc-repeats = 1
> lmc-gibbsdelta = -1
> lmc-forced-nstart = 0
> symmetrized-transition-matrix = no
> nst-transition-matrix = -1
> mininum-var-min = 100
> wl-scale = 0.6
> wl-ratio = 0.8
> init-wl-delta = 1
> wl-oneovert = yes
> Besides this I use LINCS to constrain all bonds, sd-integrator and a "normal" cut-off scheme with a 1 fs time step.
> However, once I try to run the files on the cluster I always end up with LINCS warnings and after a few seconds the program crashes due to too many LINCS warnings. If I increase the time step to 2 fs I run into problems SETTLE for the water. I always start from a nice structure that is taken as the final snap shot from a simple 1 ns MD simulation of my system.
> What could be the problem?
> If I use free_energy = yes instead of EE things work fine.
> Did I perhaps mess up the EE settings or something?
> Thanks in advance.
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